PROJECT SUMMARY The Sonic hedgehog (SHH) pathway is necessary for multiple steps of craniofacial development. Mutations in this pathway lead to devastating birth defects including holoprosencephaly and Pallister-Hall syndrome. Furthermore, a spectrum of diseases collectively referred to as craniofacial ciliopathies, are caused by ciliary mutations that affect the processing of GLI proteins, the transcriptional effectors of the pathway. This disruption in processing often leads to a reduction in both GLI activator (GLI-A) and GLI repressor (GLI-R). While GLI-A is necessary for activation of several transcriptional SHH targets, most genes are in fact activated by the de- repression of GLI-R. Despite a clear genetic requirement for GLI-R in craniofacial development, the mechanisms by which it elicits repression are undefined. This proposal aims to fill a fundamental gap in our understanding of how GLI-R proteins maintain transcriptional repression during craniofacial development. Specifically, I seek to determine if GLI repression regulates transcription by regulating epigenetic markers and by physically altering chromatin structure in terms of chromatin accessibility and GLI enhancer-promoter interactions. I hypothesize that GLI-R recruits HDACs to maintain GLI enhancers in an epigenetically repressed state with restricted chromatin accessibility and prevents GLI enhancer-promoter interactions from being established. The experiments in this proposal will provide direct mechanistic insight into the processes underlying the transcriptional regulation of SHH target genes. By identifying GLI-bound enhancers regulated by SHH signaling in craniofacial patterning, it will also serve as a resource for other scientists studying SHH regulation. !